3AGN

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 Complexed with adenosine 3'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RTUPDB ENTRY 1RTU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.7529312.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9837.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.88α = 90
b = 39.789β = 114.99
c = 35.884γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 4r2010-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.978Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.9634.398.90.05272.214.7585438
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.960.98486.30.2957.4353749

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1RTU0.9631.0558481294998.760.1180.1170.127RANDOM6.48
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.064
r_dihedral_angle_3_deg12.389
r_dihedral_angle_1_deg7.071
r_dihedral_angle_4_deg4.071
r_angle_other_deg3.562
r_scangle_it2.803
r_angle_refined_deg2.405
r_scbond_it2.16
r_mcangle_it1.691
r_mcbond_it1.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.064
r_dihedral_angle_3_deg12.389
r_dihedral_angle_1_deg7.071
r_dihedral_angle_4_deg4.071
r_angle_other_deg3.562
r_scangle_it2.803
r_angle_refined_deg2.405
r_scbond_it2.16
r_mcangle_it1.691
r_mcbond_it1.122
r_rigid_bond_restr0.735
r_mcbond_other0.287
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms870
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing